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A novel topology for representing protein folds
Author(s) -
Segal Mark R.
Publication year - 2009
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.90
Subject(s) - topology (electrical circuits) , protein folding , network topology , protein structure prediction , contact order , folding (dsp implementation) , mathematics , protein structure , computer science , physics , combinatorics , engineering , nuclear magnetic resonance , electrical engineering , operating system
Various topologies for representing 3D protein structures have been advanced for purposes ranging from prediction of folding rates to ab initio structure prediction. Examples include relative contact order, Delaunay tessellations, and backbone torsion angle distributions. Here, we introduce a new topology based on a novel means for operationalizing 3D proximities with respect to the underlying chain. The measure involves first interpreting a rank‐based representation of the nearest neighbors of each residue as a permutation, then determining how perturbed this permutation is relative to an unfolded chain. We show that the resultant topology provides improved association with folding and unfolding rates determined for a set of two‐state proteins under standardized conditions. Furthermore, unlike existing topologies, the proposed geometry exhibits fine scale structure with respect to sequence position along the chain, potentially providing insights into folding initiation and/or nucleation sites.